seqnr

seqnr

seqnr converts redundant database results to a non-redundant set of hits.

This is part of Jon Ison's protein structure analysis package. This package is still being developed. Please ignore this program until further details can be documented. All further queries should go to Jon Ison (jison@hgmp.mrc.ac.uk).

Here is a sample session with seqnr:

% seqnr

Mandatory qualifiers:

[-inf] (infile)

Name of the scop hits file (input).

[-vinf] (infile)

Name of validation file (input).

-scopin (infile)

Name of scop classification file (EMBL format input).

-alignpath (string)

Location of scop alignment files (input).

-alignextn (string)

Extension of scop alignment files.

-datafile (matrixf)

This is the scoring matrix file used when comparing sequences.

-thresh (float)

The percentage sequence identity redundancy threshold.

-mode (menu)

Select mode.

[-outf] (outfile)

Name non-redundant scop hits file (output).

[-voutfname] (string)

Name of processed validation file (output).

-logf (outfile)

Name seqnr log file (output).

Advanced qualifiers:

-gapopen (float)

The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences.

-gapextend (float)

The gap extension penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. You can usually expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception occurs when one or both sequences are single reads with possible sequencing errors, in which case you should expect many single base gaps. You can obtain this result by setting the gap open penalty to zero (or a very low value) and using the gap extension penalty to control gap scoring.



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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